Thanks Reinier,
   For posterity ended up just doing the following:

matplotlib.interactive(True)
...
s = ax.scatter(data1, data2, data3)
draw()
s.remove()
s = ax.scatter(data4, data5, data6)
draw()


>Hi Ryan,
>
>This is currently not supported. Since also the 2D PatchCollection does not 
>support it I >don't see how to easily add it either...
>
>Cheers,
>Reinier

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